A central challenge for systems biology is to transform the data deluge characteristic of the post- genomic world, into the kind of knowledge that will lead to advances in biomedical science and clinical medicine. The transformation requires computer systems that will enable organizing, mining, analyzing and displaying the data in a manner that both informs and drives new hypotheses. VisANT (a visualization, mining system) and Predictome (an integrated database component) form an online graphical workspace and interface for principled integration, mining, discovery, and analysis of molecular networks. The system currently includes, or seamlessly accesses, data sets based on some 70 laboratory and computational methods, and more than 100 species. It has a distinguished and active advisory Board, more than 1000 registered users, is accessed by more than 1100 independent sites per month and has been cited approximately 300 times in the scientific literature. We propose substantially expanding the range of VisANT by including metabolic, chemical reaction, drug and disease related data. Equally importantly, a central goal of VisANT has been integration, and we will substantially extend its integrative capabilities, enabling the identification of disease related pathways, of similarities in mechanisms between phenotypically distinct diseases, and the identification of potential lead compounds for therapy. At the same time we propose substantial expansion of our outreach activities, and movement toward a true many-to many communication and discovery system.